Visual analysis for space–time aggregation of biomolecular simulations

Abstract

Conducting a current through a nanopore allows for the analysis of molecules inside the pore because a current modulation caused by the electrostatic properties of the passing molecules can be measured. This mechanism shows great potential for DNA sequencing, as the four different nucleotide bases induce different current modulations. We present a visualisation approach to investigate this phenomenon in our simulations of DNA within a nanopore by combining state-of-the-art molecular visualisation with vector field illustration. By spatial and temporal aggregation of the ions transported through the pore, we construct a velocity field which exhibits the induced current modulations caused by ion flux. In our interactive analysis using parametrisable three-dimensional visualisations, we encountered regions where the ion motion unexpectedly opposes the direction of the applied electric field.